Oncotarget

Research Papers:

Development of a targeted sequencing approach to identify prognostic, predictive and diagnostic markers in paediatric solid tumours

Elisa Izquierdo, Lina Yuan, Sally George, Michael Hubank, Chris Jones, Paula Proszek, Janet Shipley, Susanne A. Gatz, Caedyn Stinson, Andrew S. Moore, Steven C. Clifford, Debbie Hicks, Janet C. Lindsey, Rebecca M. Hill, Thomas S. Jacques, Jane Chalker, Khin Thway, Simon O’Connor, Lynley Marshall, Lucas Moreno, Andrew Pearson, Louis Chesler, Brian A. Walker and David Gonzalez De Castro _

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Oncotarget. 2017; 8:112036-112050. https://doi.org/10.18632/oncotarget.23000

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Abstract

Elisa Izquierdo1,2, Lina Yuan1, Sally George3,4, Michael Hubank1, Chris Jones2, Paula Proszek1, Janet Shipley5, Susanne A. Gatz4,5, Caedyn Stinson6, Andrew S. Moore6,7,8, Steven C. Clifford9, Debbie Hicks9, Janet C. Lindsey9, Rebecca M. Hill9, Thomas S. Jacques10,11, Jane Chalker12, Khin Thway13, Simon O’Connor14, Lynley Marshall4, Lucas Moreno4,15, Andrew Pearson4, Louis Chesler3,4, Brian A. Walker1,16,* and David Gonzalez De Castro1,17,*

1Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, United Kingdom

2Glioma Team, Division of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom

3Paediatric Tumour Biology, Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom

4Paediatric Drug Development Team, Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom

5Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom

6The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia

7Oncology Service, Children’s Health Queensland Hospital and Health Service, Brisbane, Australia

8UQ Child Health Research Centre, The University of Queensland, Brisbane, Australia

9Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, United Kingdom

10Department of Histology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom

11Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, United Kingdom

12Haematology, Cellular and Molecular Diagnostics Service, UCL GOS Institute of Child Health, London, United Kingdom

13Sarcoma Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom

14Haemato-Oncology Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom

15HNJ-CNIO Clinical Research Unit and Hospital Universitario Niño Jesus, Madrid, Spain

16Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA

17Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom

*These authors have contributed equally to this work

Correspondence to:

David Gonzalez De Castro, email: D.GonzalezdeCastro@qub.ac.uk

Keywords: childhood cancer; targeted sequencing; molecular diagnostics; panel validation; targeted therapies

Received: July 28, 2017     Accepted: November 16, 2017     Published: December 06, 2017

ABSTRACT

The implementation of personalised medicine in childhood cancers has been limited by a lack of clinically validated multi-target sequencing approaches specific for paediatric solid tumours. In order to support innovative clinical trials in high-risk patients with unmet need, we have developed a clinically relevant targeted sequencing panel spanning 311 kb and comprising 78 genes involved in childhood cancers. A total of 132 samples were used for the validation of the panel, including Horizon Discovery cell blends (n=4), cell lines (n=15), formalin-fixed paraffin embedded (FFPE, n=83) and fresh frozen tissue (FF, n=30) patient samples. Cell blends containing known single nucleotide variants (SNVs, n=528) and small insertion-deletions (indels n=108) were used to define panel sensitivities of ≥98% for SNVs and ≥83% for indels [95% CI] and panel specificity of ≥98% [95% CI] for SNVs. FFPE samples performed comparably to FF samples (n=15 paired). Of 95 well-characterised genetic abnormalities in 33 clinical specimens and 13 cell lines (including SNVs, indels, amplifications, rearrangements and chromosome losses), 94 (98.9%) were detected by our approach. We have validated a robust and practical methodology to guide clinical management of children with solid tumours based on their molecular profiles. Our work demonstrates the value of targeted gene sequencing in the development of precision medicine strategies in paediatric oncology.


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